From academia to a country-wide response: contribution of university laboratories on the surveillance of emerging viruses in South America

Introduction

Emerging and re-emerging viruses remain a persistent threat to global public health (1). Over the past two decades, many infectious agents have emerged or re-emerged (2), posing challenges to health systems worldwide. The World Health Organization (WHO) has published a list of priority pathogens likely to cause future outbreaks (3). In Latin America (LATAM), viruses from the Orthomyxoviridae, Flaviviridae, Coronaviridae and Hantaviridae, families, among others, have been highlighted (3). These pathogens have produced a considerable burden in the region, not only through direct morbidity and mortality but also by disrupting economies and social structures. For example, the 2009 influenza pandemic led to widespread hospitalizations and strained healthcare systems (4). Recurrent dengue epidemics continue to generate substantial economic and health incidence in the Americas, which has increased by 85,5% over the past 30 years, with 2019 recording the most significant outbreaks to date (5).

The recent coronavirus disease 2019 (COVID-19) pandemic demonstrated the extraordinary capacity of a novel pathogen to spread rapidly and exposed critical weaknesses in national systems for detection, response, and control. In this context, the WHO hub for Pandemic and Epidemic Intelligence has proposed collaborative surveillance as an innovative approach to strengthening the global health architecture for emergency preparedness and response (6). However, in many countries, governmental infrastructures are insufficient to meet large-scale emergencies. These limitations underscore the need for collaborative models integrating multiple actors, including governmental agencies, hospitals, Academic/Research institutions, and universities. Chilean efforts during the pandemic showed an example of success where the universities were called to contribute to the genomic surveillance across a well-coordinated expansion program, “Programa de Aceleración de Vigilancia Genomica” that involved the direction of the national authorities of health, the execution by highly prepared university laboratories, and the financial support of private industries (7). The Chilean COVID-19 surveillance support case is only one example of the academic contribution to pathogen surveillance. This study describes the contribution of some LATAM university laboratories to nationwide viral surveillance. We also analyze their role during the COVID-19 pandemic and highlight their ongoing involvement in the surveillance of other high-impact viral pathogens such as dengue and highly pathogenic avian influenza (HPAIV).

Emerging virus outbreaks and their relevance in Latin America

In 1986, the United States Centers for Disease Control and Prevention (CDC) defined health surveillance as the ongoing systematic collection, analysis, and interpretation of health data essential to the planning, implementation, and evaluation of public health practice, closely integrated with the timely dissemination of these data to those who need to know (8). Since then, surveillance has become a cornerstone tool for the early detection of infectious diseases and evidence-based decision-making. This framework has proven particularly critical in emerging viruses, especially those of zoonotic origin, which have triggered several major outbreaks in LATAM and worldwide (Figure 1). These include the 2009 influenza pandemic caused by a swine-origin A(H1N1)pdm09 virus, the 2019 dengue outbreak transmitted by Aedes aegypti, the ongoing COVID-19 pandemic, suspected to have originated from animals such as pangolins, bats, or possibly other mammals (9, 10) and the emergence of the HPAIV A/H5N1 which since 2022 has affected poultry, migratory aquatic birds and marine mammals and currently poses a high zoonotic risk. Surveillance challenges are even greater in regions like LATAM, where high biodiversity, tropical climates, and densely populated urban areas facilitate the emergence and spread of pathogens. For these reasons, international organizations have promoted a more integrated surveillance framework based on the One Health approach, which aims to combine data of pathogens, human and animal hosts, environmental factors, and social determinants within an interdisciplinary system for early detection and response (8).

The CDC estimated that 151,700–575,400 people worldwide died during the first year of the pandemic caused by the A(H1N1)pdm09 virus (11). In LATAM, thirty-five countries reported between April and September a total of 124,219 laboratory-confirmed cases and 2,638 deaths, although these figures likely underestimate the true burden of disease (12). Additionally, several Latin American countries reported significant economic losses (12). In Chile, for example, it was estimated that the pandemic increased the mean number of workdays missed by 0.04 days per person-month, a 700-800% increase compared to non-pandemic years. Calculations based on these estimates imply a minimum 0.2% reduction in Chile’s labor supply (13). These findings underscore how an influenza outbreak can impose both health and economic burdens on societies. In this context, the recent spread of HPAIV A/H5N1 clade 2.3.4.4b (HPAIV A/H5N1) has had a devastating impact, not only economically, due to the massive losses in poultry industry, farmer livelihoods, and international trade (14), but also ecologically because of the high mortality among coastal birds and the virus´s increasing ability to infect marine mammals (15). Moreover, several groups have documented mammal-to-mammal transmission events in South America (15–18), leading scientists to question whether humans could be next (19). Globally, from 1 January 2003 to 29 September 2025, 991 cases of human infection with HPAIV A/H5N1 were reported from 25 countries, resulting in 476 deaths (a case fatality rate of 48%) (20). Notably, two human cases were confirmed in South America in 2023, one in Ecuador and one in Chile (15), highlighting the continuing risk of zoonotic transmission. On the other hand, the dengue virus (DENV), a Flavivirus transmitted by mosquitoes, represents the most significant arboviral infection in human, with cyclical outbreaks occurring every three to five years across Latin America (21, 22). Over the past four decades, reported dengue cases in LATAM have risen sharply, from 1.5 million between 1080 and 1989 to 17.5 million between 2010 and 2019. Before 2023, the largest dengue outbreak in the region occurred in 2019, with over 3.18 million reported infections, 28,208 severe cases, and 1,823 deaths, representing a case fatality rate of 0.06% (23). The economic burden of dengue is substantial, affecting individuals, communities, and national economies; the average annual cost of dengue has been estimated at approximately USD 3 billion (24). In Brazil alone, the economic impact of a major outbreak reached USD-876 million, equivalent to 0,05% of the national GDP, with the most significant losses observed in industries contributing most substantially to baseline GDP having the most impact on GDP due to dengue (24).

Finally, COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), initially emerged in Asia before rapidly spreading to other regions worldwide. LATAM remained largely unaffected until February 25, 2020 when the Brazilian Ministry of Health confirmed the first case (25). As of September 28, 2025, according to WHO data, more than 90 million confirmed cases and over 1.8 million deaths have been reported in the region (26). Moreover, the COVID-19 pandemic occurred during a period of economic stagnation and macroeconomic vulnerability in the region (27). In 2020, global gross domestic product (GDP) declined by approximately 2.0%, while LATAM experienced a much sharper contraction of 5.3%, resulting in nearly 30 million additional people falling into poverty (28). During the pandemic, several animal species were also found to be infected with SARS-CoV-2, including domestic cats and dogs, as well as animal kept in rehabilitation centers or zoological institution such as monkeys, common woolly monkey, hairy armadillo, coat, tiger, according to reports from Brazil, Chile, Argentina, Panama, Ecuador, and Mexico (29–35).

Together, the influenza A(H1N1)pdm09, DENV, SARS-CoV-2 and (HPAIV) A/H5N1 outbreaks exemplify how viruses with distinct transmission dynamics, host ranges, and ecological determinants can differently impact public health across LATAM. Their combined effects underscore the urgent need for integrated surveillance and coordinated policy responses capable of addressing both emerging and re-emerging viral threats.

Surveillance of emerging and high-impact viruses in Latin America

Genomic surveillance plays a key role during the emergence or re-emergence of viruses within a population, enabling improved response and decision-making in both epidemic and pandemic contexts. To better understand these contributions, we reviewed a dataset generated from the GISAID repository for the human sequences for Influenza A(H1N1) pdm09, DENV, SARS-CoV-2 and, sequences of the recent HPAIV A/H5N1 outbreak viruses (Supplementary Tables 1-4). This review enabled us to visualize the contributions of LATAM universities by downloading all available sequences from each virus key outbreak periods: A(H1N1)pdm09 (200–2010), DENV (2018–2023), SARS-CoV-2 (2020–2022), and HPAIV A/H5N1 (2022–2025) (Figures 2A–D). The final dataset included 369 sequences for A(H1N1)pdm09, 398 for DENV, 364,038 for SARS-CoV-2, and 397 for HPAIV A/H5N1. During the A(H1N1)pdm09 pandemic, there are no records of university contributions between the years in which the health emergency was registered on the GISAID database. (Figure 2A). For DENV, a manual review was necessary because GISAID’s metadata available for download does not include the laboratory of origin information. 10% of the total sequences from 2018–2023 (n=3,980) were randomly selected. This stratified random selection keeps the proportional contribution of each country, resulting in 398 sequences included for review. Brazil was the major contributor to DENV sequences, ~87% (Figure 2B). Of these, only 82 sequences were uploaded by universities, and 67 were uploaded at least one year after sample collection. On the other hand, during the SARS-CoV-2 emergency, the contribution of LATAM universities was ~10% of the total published sequences. Brazil shows the largest university contribution of sequences for SARS-CoV-2 (15865 seq/35849 seq or 44.2%) followed by Colombia (7926 seq/35849 seq, or 22.1%), Chile (4897 seq/35849 seq, or 13.6%), and Peru (2726 seq/35849 seq, or 7.6%), respectively (Figure 2C).

In contrast, for HPAIV A/H5N1, universities made greater contributions, accounting for more than 50% of the total sequences published during the review period. Most sequences to date belonging to Chile (70%) (Figure 2D). Additionally, for both A(H1N1) pdm09 and HPAIV A/H5N1, a portion of sequences -61.7% and 15.6%, respectively- could not be assigned to any institution, whether academic or public, due to incomplete metadata on GISAID database.

In the case of the DENV and SARS-CoV-2 outbreaks, universities’ contributions were lower during the first semester than during the rest of the period. In contrast, during the HPAIV A/H5N1 emergency, universities made the greatest contribution during the first semester of the outbreak, both relative to the rest of the period and to other institutions. During the DENV outbreak, two peaks were observed. The first peak occurred in 2019, during which the first six months saw universities contribute 49% of the total sequences, versus 51% from other institutions. If we also consider the increase in cases since November 2018, the contribution from universities was 43.6%, versus 56.4% from other institutions. As in the overall picture, Brazil was the country with the greatest contribution from universities, accounting the 91% of the total sequences uploaded by universities during the first semester. In the case of SARS-CoV-2, during the first semester of the emergency, universities contributed 24.5% of the total sequences available that semester, compared to 75.5% uploaded by other institutions. As with DENV, Brazil was the country that contributed the most, accounting for 65.7% of the total sequences uploaded by universities.

Finally, for HPAIV A/H5N1, universities contributed 49.6% of the sequences, compared to 28% from other institutions, while the remaining 22.4% correspond to sequences uploaded by unidentified institutions. In contrast to DENV and SARS-CoV-2, the country with the largest university contribution in the first half of the emergency was Chile, with 81.5% of the sequences available during that period.

Contribution of academia to the outreach of surveillance data

University laboratories in Latin America made measurable and actionable contributions to surveillance data in the most relevant periods where the respective outbreaks of each virus reviewed occurred. To determine the LATAM countries contribution to the outreach, a PubMed search was performed to identify scientific articles in which collection was associated with outbreaks of A(H1N1) pdm09, DENV, SARS-CoV-2 and HPAIV A/H5N1 and keywords including genomic surveillance, molecular surveillance, outbreaks, and each virus name, combined with Latin America or specific country names, using Boolean operators (AND, OR). Articles published in English between 2009 and 2025 were included. Publications were excluded if they referred to the target viruses but were not linked to outbreak periods or did not involve epidemiological or genomic surveillance activities. Over the periods analyzed, our compilation of 43 peer-reviewed and pre-print studies, considering 10 LATAM countries, demonstrates the substantial role of academic laboratories in genomic surveillance, with 32 of the total studies generated or analyzed by university groups (Table 1). Their central role has not only been for data production but for knowledge creation, local decision-making, and translational outputs.

Table 1. Institutional collaboration and scientific output in viral surveillance during major outbreaks in Latin America.

Natl., national; Natl/Intl., National with International collaboration; Intl., International collaborations.

The academia contributed in three major dimensions: first, rapid generation and deposition of whole-genome sequences, enabling early detection of introductions of emerging viruses locally and their local transmission chains (37, 46, 47, 51, 75). Second, phylogenetic and epidemiological analysis to generate locally relevant knowledge to inform national decision-making regarding the emergence of a virus (15, 17, 18, 36, 43, 46, 52, 60) and third, capacity building through implementation of sequencing workflow within the academic laboratories, highlighting this efforts of Chile, Bolivia and Paraguay where university laboratories contributed with the development of economical and scalable molecular protocols (42, 52, 69, 77). This, coupled with technical training for national teams, helped generate surveillance data at the national level. The long-term investment allowed for the maintenance of the sequencing capacity beyond outbreaks of the viruses, ensuring continued monitoring of viral pathogens. Regarding scientific output related specifically to surveillance, Chile contributed nine studies (n=9) followed by Brazil and Colombia (n=8), Argentina (n=7) and Bolivia, Ecuador, Panama, Paraguay, Peru and Uruguay with at least 1 per country. Across viruses, SARS-CoV-2 accounted for the largest number of publication, with twenty-one studies, followed by HPAIV A/H5N1 (n=13); DENV, mainly represents in countries with higher disease burden such Brazil and Colombia and finally pandemic influenza A(H1N1) pdm09 with four studies.

Additionally, approximately 28% of the identified studies involved international collaboration, with 82% from institutions in the Northern Hemisphere and 18% representing intra-LATAM countries (Supplementary Table 5). Example such as the support provided by Chilean universities to Bolivia for SARS-CoV-2 sequencing (42), or the collaboration between Uruguay and Brazil during the same emergency (39), illustrate how regional partnership helped sustain surveillance capacity in setting with limited infrastructure.

Discussion

This study reveal that, during the major epidemic and pandemic outbreaks of the last two decades, including the 2009 influenza A(H1N1) pdm09 pandemic, the 2019 DENV epidemic, the 2020 SARS-CoV-2 pandemic, and the ongoing highly pathogenic avian influenza emergency, Latin America has faced not only profound impacts on health and economy but also demonstrated the pivotal role of integrate the academic institutions to strength the surveillance capacities. Through the implementation of sequencing platforms, genomic analysis, and the training of specialized technical personnel, university laboratories complemented national public health systems, enabling more timely detection of viral circulation and the emergence of new variants. Notably, universities contributed substantially to genomic surveillance, accounting for between 10% and 50% of all sequences deposited in international databases (Figure 2). This contribution underscores the scientific and technical capacity of academia and its readiness to respond to future health emergencies.

The LATAM experience demonstrates that collaboration between universities, public health agencies, and international research centers was the key to improving response capacity during outbreaks. Countries such as Chile, Brazil, and Argentina exemplify how cooperation between academic institutions and ministries of health enabled the expansion of genomic surveillance, ultimately supporting data-driven public health decisions. It’s important to highlight that this collaborations also expand the borders of continental territories in South America, and includes the pristine Antarctic continent, where integral contributions of LATAM academia and national institutions, especially the Instituto Antarctica Chileno (INACH) favored monitoring the introduction and dissemination of the HPAIV/H5N1 (78, 79). Collaborations with CEIRR-funded center such as the Ichan School of Medicine at Mount Sinai, Emory University and St. Jude Children’s Research Hospital as well as other universities and international partners, including University of Maryland (USA), UC Davis (USA), Robert Koch Institute (Germany), Imperial College-London (UK), Oxford University (UK) (Supplementary Figure 5) were instrumental in generating high-quality studies, strengthening bioinformatics analyses, and fostering scientific dissemination.

Despite the advances, structural challenges continue to limit the potential of genomic surveillance in the region. Among them are the lack of standardized metadata, delays between sample collection and sequence publication, and incomplete information regarding the origin or submission date of the sample. These issues were particularly evident in influenza A(H1N1) pdm09 and HPAIV A/H5N1 datasets, highlighting the need for regional mechanisms to ensure traceability and timely data availability. Furthermore, academic incentives to publish may sometimes delay the public release of sequences, reducing their utility for rapid public health decision-making. It’s important to note that some databases, like GISAID, import metadata for sequences from other public repositories, as GenBank. In this process, it´s possible to observe a loss of information in some sections, as we saw in this paper for the originating and submitting labs. This could be a problem for the utility of the data and the recognition of teams that generate them.

The comparative analysis of the viruses included in this study revealed a progressive increase in the participation of universities during epidemic and pandemic outbreaks. For instance, whole academic involvement in surveillance was minimal during the 2009 influenza pandemic; it expanded during the SARS-CoV-2 pandemic and reached a leading role in the highly pathogenic avian influenza outbreaks. This pattern likely reflects the substantial strengthening of scientific infrastructure and technical training achieved after COVID-19 and the growing academic interest in publishing research on zoonotic viruses of high regional relevance. In Chile, for example, universities contributed over 70% of highly pathogenic avian influenza sequences reported to international databases, highlighting both academic institutions’ technical maturity and scientific commitment. These differences also suggest that the sustainability of surveillance efforts largely depends on institutional incentives, funding availability, and academia’s integration within national public health strategies.

Over time, academia’s growing involvement has demonstrated that when viewed integrally and collaboratively, it not only generates surveillance data but builds autonomy at a local level–democratizing science and making it relevant to each country’s reality. This empowers countries to obtain their own data to analyze it and make policy decisions rather than relying on external extrapolations and other countries’ responses. For example, in Paraguay, the Institute for Health Sciences Research (IICS) at the National University of Asunción established a contingency diagnostic laboratory for COVID-19, which became the main testing center for a major university hospital. The IICS team adapted protocols and developed a cost-effective and scalable molecular approach for variant surveillance (69, 70). Similar efforts were performed in Bolivia by the Instituto de Investigaciones Biomédicas (IIBISMED), Universidad Mayor de San Simón (42). These efforts enabled genomic monitoring under resource-constrained conditions and exemplified the valuable support of Universities during the pandemic.

SARS-CoV-2 pandemic revealed significant inequalities between countries, both in the volume of sequencing and in the participation of the university sector. Brazil and Peru contributed the largest number of total sequences, while Bolivia and Guyana contributed the fewest. In terms of academic output, Brazil and Colombia led in the absolute number of sequences generated by universities; however, when considering the percentage originating from universities relative to the total for each country, Bolivia (87.14%) and Colombia (53.88%) accounted for the largest proportion of sequences originating from academic institutions, in contrast to Brazil (7.41%), Peru (6.01%), and Guyana (6.98%) (Supplementary Table 6). These differences appear to be associated with the structural capacity of the scientific and healthcare systems, as reflected in economic and human development indicators. In 2021, countries with higher income and development levels, such as Chile (GNI per capita 27,407 PPP$, HDI 0.865) and Uruguay (GNI per capita 26,279 PPP$, HDI 0.837), also had the highest testing rates in the region (1,468.3 and 1,448.6 tests per 1,000 people, respectively), well above countries like Brazil (308.5) or Bolivia (290) ( (80)). This greater diagnostic effort is partially reflected in the diagnosis-sequencing ratio, where Peru achieved the highest sequencing percentage relative to the total number of confirmed cases (1.001%), followed by Chile (0.715%), while Uruguay (0.144%) and Bolivia (0.032%) had considerably lower proportions (80, Supplementary Table 6). However, even in the countries with the best relative performance, these values remained low, suggesting that during the peak of the pandemic—even with the mobilization of extraordinary resources to strengthen genomic surveillance—diagnostic and sequencing systems quickly reached their operational limits. In this context, diagnostic capacity emerges as a key, though scarcely discussed, determinant of genomic information generation during health emergencies.

The result of this revision demonstrates that Latin American academia has been an essential component of recent public health responses, bridging the gap between science, public health, and policymaking. The sustained integration of academic institutions into surveillance frameworks will ensure preparedness for future epidemics and pandemics, strengthen regional autonomy, and foster evidence-based decision-making tailored to local realities.

Therefore, university laboratories should be recognized as permanent actors within national surveillance systems, not merely as emergency resources. Integrated detection programs under the One Health approach reinforce the importance of establishing collaborative, sustainable, and multisectoral systems. Uneven capabilities across countries create disparities in the representation of genomic data, with better-resourced institutions able to contribute more consistently than those with limited infrastructure. Sustainability remains a challenge, as surveillance efforts depend on short funding cycles, limited personnel incentives, and fragile integration of academic laboratories within national public health systems. Addressing these limitations will require standardized metadata requirements, regional capacity building initiatives, and long term investment strategies to ensure that academic contributions remain a stable and integral part of national surveillance frameworks. in this context, regional progress should align with international initiatives, such as the WHO’s Collaborative Surveillance strategy to promote sustained monitoring, equitable data sharing, and rapid response capabilities (6).

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Supplementary material

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fviro.2026.1755747/full#supplementary-material

Supplementary material Supplementary material at the source

Footnotes

Edited by: Víctor Hugo Fernández-Bedoya, Universidad Nacional Mayor de San Marcos, Peru

Reviewed by: Sanjay Lamba, Institute for Stem Cell Biology and Regenerative Medicine, India

Florencia Del Puerto, Universidad Nacional de Asunción, Paraguay